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Nano breathers and molecular dynamics simulations in hydrogen-bonded chains

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Abstract

Non-linear localization phenomena in biological lattices have attracted a steadily growing interest and their existence has been predicted in a wide range of physical settings. We investigate the non-linear proton dynamics of a hydrogen-bonded chain in a semi-classical limit using the coherent state method combined with a Holstein–Primakoff bosonic representation. We demonstrate that even a weak inherent discreteness in the hydrogen-bonded (HB) chain may drastically modify the dynamics of the non-linear system, leading to instabilities that have no analog in the continuum limit. We suggest a possible localization mechanism of polarization oscillations of protons in a hydrogen-bonded chain through modulational instability analysis. This mechanism arises due to the neighboring proton–proton interaction and coherent tunneling of protons along hydrogen bonds and/or around heavy atoms. We present a detailed analysis of modulational instability, and highlight the role of the interaction strength of neighboring protons in the process of bioenergy localization. We perform molecular dynamics simulations and demonstrate the existence of nanoscale discrete breather (DB) modes in the hydrogen-bonded chain. These highly localized and long-lived non-linear breather modes may play a functional role in targeted energy transfer in biological systems.

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Acknowledgements

One of the authors, L. K., gratefully acknowledges the financial support from UGC, NBHM, India, in the form of major research projects, BRNS, India, in the form of a Young Scientist Research Award and ICTP, Italy, for a Junior Associateship. A. M. gratefully acknowledges UGC for the Rajiv Gandhi National Fellowship. This research work was partially supported by Serbian Ministry of Education and Sciences (grant III45010).

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Authors and Affiliations

  1. Department of Physics, Periyar University, Salem, 636 011, India

    L. Kavitha, A. Muniyappan, A. Prabhu & S. Jayanthi

  2. The Abdus Salam International Centre for Theoretical Physics, Trieste, Italy

    L. Kavitha

  3. Center for Nanoscience and Nanotechnology, Periyar University, Salem, 636 011, Tamilnadu, India

    L. Kavitha & D. Gopi

  4. Institut za nuklearne nauke Vinča, Univerzitet u Beogradu, Poštanski fah 522, 11001, Beograd, Serbia

    S. Zdravković

  5. Department of Chemistry, Periyar University, Salem, 636 011, India

    D. Gopi

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  1. L. Kavitha
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Kavitha, L., Muniyappan, A., Prabhu, A. et al. Nano breathers and molecular dynamics simulations in hydrogen-bonded chains. J Biol Phys 39, 15–35 (2013). https://doi.org/10.1007/s10867-012-9283-7

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